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Cited by 7Cellular transport and secretionSARS-CoV-2 and COVID-19 ResearchAutophagy in Disease and Therapy

Acidic pH of early endosomes governs SARS-CoV-2 transport in host cells

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Fares, Perla, Duhaini, Mariam, Tripathy, Suvranta K., Srour, Ali, Kondapalli, Kalyan C.·2025·Journal of Biological Chemistry
DOI 10.1016/j.jbc.2024.108144PMC PMC11815683
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Abstract

Endocytosis is a prominent mechanism for SARS-CoV-2 entry into host cells. Upon internalization into early endosomes (EEs), the virus is transported to late endosomes (LEs), where acidic conditions facilitate spike protein processing and viral genome release. Dynein and kinesin motors drive EE transport along microtubules; dynein moves EEs to the perinuclear region, while kinesins direct them towards the plasma membrane, creating a tug-of-war over the direction of transport. Here, we identify that the luminal pH of EEs is a key factor regulating the outcome of this tug-of-war. Among the known endosomal pH regulators, only the sodium-proton exchanger NHE9 has so far been genetically linked to severe COVID-19 risk. NHE9 functions as a proton leak pathway specifically on endosomes. We show that limiting acidification of EEs by increasing the expression of NHE9 leads to decreased infectivity of the SARS-CoV-2 spike-bearing virus in host cells. Our investigation identified the EE membrane lipid phosphatidylinositol-3-phosphate (PI3P) as a link between luminal pH changes and EE transport. Normally, as EEs mature, PI3P depletes. However, in cells with high NHE9 expression, PI3P persists longer on EEs. PI3P plays a pivotal role in the recruitment of motor proteins and the subsequent movement of EEs. Consistently, we observed that NHE9-mediated alkalization of EEs hindered perinuclear movement. Specifically, EE speed and run length were negatively impacted, ultimately leading to EEs falling off microtubules and impairing the delivery of viral cargo to LEs. NHE9 thus offers a unique opportunity as a viable therapeutic target to impede SARS-CoV-2 host cell entry.

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  • Internalized cargo localizes to late endosomes approximately 10 minutes after uptake.

    “previous studies established that internalized cargo localizes to late endosomes ~10 minutes after uptake29–31”

    From INPP5D/SHIP1 regulates endo-lysosomal function and cargo-selective phagocytosis in human microglia (2025) · cites this paper as [29]

    The Results section on viral cargo delivery reports colocalization of internalized SARS-CoV-2 spike protein with the late-endosome marker Rab7 at 20 minutes after internalization (page not provided). It supports late-endosomal localization for that cargo, but not the claim’s approximately 10-minute timing or its generalization to internalized cargo broadly. (LLM, conf=0.86)

    Experimental — accuracy not yet measured

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  1. [1]Li Q. Guan X. Wu P. Wang X. Zhou L. Tong Y. Early transmission dynamics in Wuhan, China, of novel coronavirus-infected Pneumonia N. Engl. J. Med. 382 2020 1199 1207 31995857 PMC7121484
  2. [2]Wang C. Horby P.W. Hayden F.G. Gao G.F. A novel coronavirus outbreak of global health concern Lancet 395 2020 470 473 31986257 PMC7135038
  3. [3]Velazquez-Salinas L. The complex evolutionary dynamics of SARS-CoV-2, a big challenge to control the pandemic of COVID-19 J. Med. Virol. 94 2022 5082 5085 35798562 PMC9350130
  4. [4]Jackson C.B. Farzan M. Chen B. Choe H. Mechanisms of SARS-CoV-2 entry into cells Nat. Rev. Mol. Cell Biol 23 2022 3 20 34611326 PMC8491763
  5. [5]Hoffmann M. Kleine-Weber H. Schroeder S. Kruger N. Herrler T. Erichsen S. SARS-COV-2 cell entry depends on ACE2 and TMPRSS2 and is blocked by a clinically proven protease inhibitor Cell 181 2020 271 280.e8 32142651 PMC7102627
  6. [6]Shang J. Wan Y. Luo C. Ye G. Geng Q. Auerbach A. Cell entry mechanisms of SARS-CoV-2 Proc. Natl. Acad. Sci. U. S. A. 117 2020 11727 11734 32376634 PMC7260975
  7. [7]Yang B. Jia Y. Meng Y. Xue Y. Liu K. Li Y. SNX27 suppresses SARS-CoV-2 infection by inhibiting viral lysosome/late endosome entry Proc. Natl. Acad. Sci. U. S. A. 119 2022 e2117576119 PMC8794821 35022217
  8. [8]Kreutzberger A.J.B. Sanyal A. Saminathan A. Bloyet L.M. Stumpf S. Liu Z. SARS-CoV-2 requires acidic pH to infect cells Proc. Natl. Acad. Sci. U. S. A. 119 2022 e2209514119 PMC9499588 36048924
  9. [10]Wen Z. Zhang Y. Lin Z. Shi K. Jiu Y. Cytoskeleton-a crucial key in host cell for coronavirus infection J. Mol. Cell Biol. 12 2020 968 979 32717049 PMC7454755
  10. [11]Shamroukh H.S. Lone N. Akhtar M. Altayib A. Sutliff S. Kassem Z. The sodium proton exchanger NHE9 regulates phagosome maturation and bactericidal activity in macrophages J. Biol. Chem. 298 2022 102150 PMC9293770 35716776
  11. [12]Li X. Zhu W. Fan M. Zhang J. Peng Y. Huang F. Dependence of SARS-CoV-2 infection on cholesterol-rich lipid raft and endosomal acidification Comput. Struct. Biotechnol. J. 19 2021 1933 1943 33850607 PMC8028701
  12. [13]Maxson M.E. Grinstein S. The vacuolar-type h(+)-atpase at a glance - more than a proton pump J. Cell Sci. 127 2014 4987 4993 25453113
  13. [14]Freeman S.A. Grinstein S. Orlowski J. Determinants, maintenance, and function of organellar pH Physiol. Rev. 103 2023 515 606 35981302
  14. [15]Winklemann I. Matsuoka R. Meier P.F. Shutin D. Zhang C. Orellana L. Structure and elevator mechanism of the mammalian sodium/proton exchanger NHE9 EMBO J. 39 2020 e105908 PMC7737618 33118634
  15. [16]Pedersen S.F. Counillon L. The SLC9A-C mammalian Na(+)/H(+) exchanger family: molecules, mechanisms, and physiology Physiol. Rev. 99 2019 2015 2113 31507243
  16. [17]Beydoun R. Hamood M.A. Gomez Zubieta D.M. Kondapalli K.C. Na(+)/h(+) exchanger 9 regulates iron mobilization at the blood-brain barrier in response to iron starvation J. Biol. Chem. 292 2017 4293 4301 28130443 PMC5354498
  17. [18]Kondapalli K.C. Llongueras J.P. Capilla-Gonzalez V. Prasad H. Hack A. Smith C. A leak pathway for luminal protons in endosomes drives oncogenic signalling in glioblastoma Nat. Commun. 6 2015 6289 25662504 PMC4354686
  18. [19]Kondapalli K.C. Prasad H. Rao R. An inside job: how endosomal Na(+)/H(+) exchangers link to autism and neurological disease Front Cell Neurosci. 8 2014 172 25002837 PMC4066934
  19. [20]Prasad H. Protons to patients: targeting endosomal Na(+)/H(+) exchangers against COVID-19 and other viral diseases FEBS J. 288 2021 5071 5088 34490733 PMC8646450
  20. [21]Li H.S. Stolz D.B. Romero G. Characterization of endocytic vesicles using magnetic microbeads coated with signaling ligands Traffic 17 2016 1150 27624842
  21. [22]Lee C. Kang H.J. von Ballmoos C. Newstead S. Uzdavinys P. Dotson D.L. A two-domain elevator mechanism for sodium/proton antiport Nature 501 2013 573 577 23995679 PMC3914025
  22. [23]Kondapalli K.C. Hack A. Schushan M. Landau M. Ben-Tal N. Rao R. Functional evaluation of autism-associated mutations in NHE9 Nat. Commun. 4 2013 2510 24065030 PMC3815575
  23. [24]Flessner R. Orlowski J. Na+/H+ exchangers Offermanns S. Rosenthal W. Encyclopedia of Molecular Pharmacology 2021 Springer International Publishing Cham 1047 1062
  24. [25]Bright N.A. Gratian M.J. Luzio J.P. Endocytic delivery to lysosomes mediated by concurrent fusion and kissing events in living cells Curr. Biol. 15 2005 360 365 15723798
  25. [26]Dolman N.J. Kilgore J.A. A review of reagents for fluorescence microscopy of cellular compartments and structures, part I: Bacmam labeling and reagents for vesicular structures Curr. Protoc. 3 2023 e751 37311031
  26. [27]Di Paolo G. De Camilli P. Phosphoinositides in cell regulation and membrane dynamics Nature 443 2006 651 657 17035995
  27. [28]Gruenberg J. Lipids in endocytic membrane transport and sorting Curr. Opin. Cell Biol. 15 2003 382 388 12892777
  28. [29]Jongsma M.L.M. Bakker N. Neefjes J. Choreographing the motor-driven endosomal dance J. Cell Sci. 136 2023 jcs259689 PMC9845747 36382597
  29. [30]Pathak D. Mallik R. Lipid - motor interactions: soap opera or symphony? Curr. Opin. Cell Biol. 44 2017 79 85 27697416
  30. [31]Naufer A. Hipolito V.E.B. Ganesan S. Prashar A. Zaremberg V. Botelho R.J. pH of endophagosomes controls association of their membranes with Vps34 and PtdIns(3)P levels J. Cell Biol. 217 2018 329 346 29089378 PMC5748975
  31. [32]Hammond G.R.V. DepHining membrane identity J. Cell Biol. 217 2018 19 20 29233864 PMC5748998
  32. [33]Tokunaga M. Imamoto N. Sakata-Sogawa K. Highly inclined thin illumination enables clear single-molecule imaging in cells Nat. Methods 5 2008 159 161 18176568
  33. [34]Tirumala N.A. Redpath G.M.I. Skerhut S.V. Dolai P. Kapoor-Kaushik N. Ariotti N. Single-molecule imaging of stochastic interactions that drive dynein activation and cargo movement in cells J. Cell Biol. 223 2024 e202210026 PMC10798859 38240798
  34. [35]Posey D. Blaisdell-Pijuan P. Knoll S.K. Saif T.A. Ahmed W.W. Small-scale displacement fluctuations of vesicles in fibroblasts Sci. Rep. 8 2018 13294 30185883 PMC6125338
  35. [37]Esposito F. Sorosina M. Ottoboni L. Lim E.T. Replogle J.M. Raj T. A pharmacogenetic study implicates SLC9a9 in multiple sclerosis disease activity Ann. Neurol. 78 2015 115 127 25914168
  36. [38]Daczkowski C.M. Dzimianski J.V. Clasman J.R. Goodwin O. Mesecar A.D. Pegan S.D. Structural insights into the interaction of coronavirus papain-like proteases and interferon-stimulated gene product 15 from different species J. Mol. Biol. 429 2017 1661 1683 28438633 PMC5634334
  37. [39]Yoshikawa T. Hill T.E. Yoshikawa N. Popov V.L. Galindo C.L. Garner H.R. Dynamic innate immune responses of human bronchial epithelial cells to severe acute respiratory syndrome-associated coronavirus infection PLoS One 5 2010 e8729 PMC2806919 20090954
  38. [40]Masre S.F. Jufri N.F. Ibrahim F.W. Abdul Raub S.H. Classical and alternative receptors for SARS-CoV-2 therapeutic strategy Rev. Med. Virol. 31 2021 1 9 PMC7883063 33368788
  39. [41]Granger E. McNee G. Allan V. Woodman P. The role of the cytoskeleton and molecular motors in endosomal dynamics Semin. Cell Dev. Biol. 31 2014 20 29 24727350 PMC4071412
  40. [42]Steinberg B.E. Grinstein S. Pathogen destruction versus intracellular survival: the role of lipids as phagosomal fate determinants J. Clin. Invest. 118 2008 2002 2011 18523652 PMC2396921
  41. [43]Wassmer T. Attar N. Harterink M. van Weering J.R. Traer C.J. Oakley J. The retromer coat complex coordinates endosomal sorting and dynein-mediated transport, with carrier recognition by the trans-Golgi network Dev. Cell 17 2009 110 122 19619496 PMC2714578
  42. [44]Rai A. Pathak D. Thakur S. Singh S. Dubey A.K. Mallik R. Dynein clusters into lipid microdomains on phagosomes to drive rapid transport toward lysosomes Cell 164 2016 722 734 26853472 PMC4752818
  43. [45]Gomez Zubieta D.M. Hamood M.A. Beydoun R. Pall A.E. Kondapalli K.C. MicroRNA-135a regulates NHE9 to inhibit proliferation and migration of glioblastoma cells Cell Commun. Signal 15 2017 55 29268774 PMC5740897
  44. [46]Pall A.E. Juratli L. Guntur D. Bandyopadhyay K. Kondapalli K.C. A gain of function paradox: targeted therapy for glioblastoma associated with abnormal NHE9 expression J. Cell Mol. Med. 23 2019 7859 7872 31532058 PMC6815843
  45. [47]Schneider C.A. Rasband W.S. Eliceiri K.W. NIH image to ImageJ: 25 years of image analysis Nat. Methods 9 2012 671 675 10.1038/nmeth.2089 22930834 PMC5554542 · DOI · Paper page
  46. [48]Dowling J.J. Vreede A.P. Low S.E. Gibbs E.M. Kuwada J.Y. Bonnemann C.G. Loss of myotubularin function results in T-tubule disorganization in zebrafish and human myotubular myopathy Plos Genet. 5 2009 e1000372 PMC2631153 19197364
  47. [49]Nobukuni T. Joaquin M. Roccio M. Dann S.G. Kim S.Y. Gulati P. Amino acids mediate mTOR/raptor signaling through activation of class 3 phosphatidylinositol 3OH-kinase Proc. Natl. Acad. Sci. U. S. A. 102 2005 14238 14243 10.1073/pnas.0506925102 16176982 PMC1242323 · DOI
  48. [50]Zornetta I. Brandi L. Janowiak B. Dal Molin F. Tonello F. Collier R.J. Imaging the cell entry of the anthrax oedema and lethal toxins with fluorescent protein chimeras Cell Microbiol. 12 2010 1435 1445 20438574
  49. [52]Tirumala N.A. Ananthanarayanan V. Visualization of single dynein molecules in mammalian cells methods Mol. Biol. 2623 2023 87 93 36602681
  50. [53]Jaqaman K. Loerke D. Mettlen M. Kuwata H. Grinstein S. Schmid S.L. Robust single-particle tracking in live-cell time-lapse sequences Nat. Methods 5 2008 695 702 18641657 PMC2747604
  51. [54]Tinevez J.Y. Perry N. Schindelin J. Hoopes G.M. Reynolds G.D. Laplantine E. TrackMate: an open and extensible platform for single-particle tracking Methods 115 2017 80 90 27713081

Cited by

Sorted by citations

Authors
Fares, P., Duhaini, M., Tripathy, S. K., Srour, A., & Kondapalli, K. C.
Affiliations
University of Michigan–Dearborn (US)
Corresponding author
Kondapalli, Kalyan C.
ORCID
Venue
Journal of Biological Chemistry
Publisher
Elsevier BV
Published
2025-02
Volume
301
Issue
2
Pages
108144
ISSN
0021-9258 (ISSN-L)
DOI
10.1016/j.jbc.2024.108144
PMC
PMC11815683
OpenAlex
W4405807476
Cited by
7
References
2
Citations by year
2026: 3 · 2025: 4
FWCI
1.57
Type
journal article
Language
en
Open access
Licence
Locations
  • Journal of Biological Chemistry (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
Funders
  • National Institutes of Health
  • University of Michigan-Dearborn
  • National Institute of General Medical Sciences (R16GM153701)
  • National Institute of Allergy and Infectious Diseases
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Cellular transport and secretion
  • Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 and COVID-19 Research
  • Health Sciences › Medicine › Epidemiology › Autophagy in Disease and Therapy
Keywords
SARS-CoV-2, early endosomes, endosomal pH, NHE9, endosomal acidification, phosphatidylinositol 3-phosphate, dynein, kinesin, microtubule transport, late endosomes, viral entry, COVID-19 risk, therapeutic target
MeSH terms
COVID-19, SARS-CoV-2, Animals, Chlorocebus aethiops, Endocytosis, Humans, Hydrogen-Ion Concentration, Microtubules, Endosomes, Vero Cells, Sodium-Hydrogen Exchangers, Phosphatidylinositol Phosphates, Virus Internalization, Spike Glycoprotein, Coronavirus

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